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comparison scanpy-find-variable-genes.xml @ 21:79da59a0b180 draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 69b3fd29988bdcbf30d38572b75793ab74110acd-dirty"
author ebi-gxa
date Fri, 06 Aug 2021 15:22:46 +0000
parents f952b39f0794
children 82bd7bf93454
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20:24fca62faafd 21:79da59a0b180
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="scanpy_find_variable_genes" name="Scanpy FindVariableGenes" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> 2 <tool id="scanpy_find_variable_genes" name="Scanpy FindVariableGenes" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
3 <description>based on normalised dispersion of expression</description> 3 <description>based on normalised dispersion of expression</description>
4 <macros> 4 <macros>
5 <import>scanpy_macros2.xml</import> 5 <import>scanpy_macros2.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
21 #if $span 21 #if $span
22 --span ${span} 22 --span ${span}
23 #end if 23 #end if
24 --n-bins '${n_bin}' 24 --n-bins '${n_bin}'
25 ${filter} 25 ${filter}
26 #if $batch_key
27 --batch-key ${batch_key}
28 #end if
26 @INPUT_OPTS@ 29 @INPUT_OPTS@
27 @OUTPUT_OPTS@ 30 @OUTPUT_OPTS@
28 ]]></command> 31 ]]></command>
29 32
30 <inputs> 33 <inputs>
48 <param name="span" argument="--span" type="float" min="0" max="1" value="0.3" optional="true" 51 <param name="span" argument="--span" type="float" min="0" max="1" value="0.3" optional="true"
49 label="The fraction of the data (cells) used when estimating the variance in the loess model fit if flavor='seurat_v3'"/> 52 label="The fraction of the data (cells) used when estimating the variance in the loess model fit if flavor='seurat_v3'"/>
50 <param name="n_bin" argument="--n-bins" type="integer" value="20" label="Number of bins for binning the mean expression"/> 53 <param name="n_bin" argument="--n-bins" type="integer" value="20" label="Number of bins for binning the mean expression"/>
51 <param name="filter" argument="--subset" type="boolean" truevalue="--subset" falsevalue="" checked="false" 54 <param name="filter" argument="--subset" type="boolean" truevalue="--subset" falsevalue="" checked="false"
52 label="Remove genes not marked as highly variable" help="When set, inplace subset to highly-variable genes, otherwise only flag highly-variable genes."/> 55 label="Remove genes not marked as highly variable" help="When set, inplace subset to highly-variable genes, otherwise only flag highly-variable genes."/>
53 <param name="batch_key" argument="--batch-key" type="text" label="Batch key" help="If specified, highly-variable genes are selected within each batch separately and merged. This simple process avoids the selection of batch-specific genes and acts as a lightweight batch correction method. For all flavors, genes are first sorted by how many batches they are a HVG. For dispersion-based flavors ties are broken by normalized dispersion. If flavor = 'seurat_v3', ties are broken by the median (across batches) rank based on within-batch normalized variance."/> 56 <param name="batch_key" argument="--batch-key" type="text" label="Batch key" optional="true" help="If specified, highly-variable genes are selected within each batch separately and merged. This simple process avoids the selection of batch-specific genes and acts as a lightweight batch correction method. For all flavors, genes are first sorted by how many batches they are a HVG. For dispersion-based flavors ties are broken by normalized dispersion. If flavor = 'seurat_v3', ties are broken by the median (across batches) rank based on within-batch normalized variance."/>
54 </inputs> 57 </inputs>
55 58
56 <outputs> 59 <outputs>
57 <expand macro="output_data_obj" description="Variable genes"/> 60 <expand macro="output_data_obj" description="Variable genes"/>
58 </outputs> 61 </outputs>